It would seem that Mohamed Morsy is on a roll. Less than a week after sacking several major security chiefs, the first elected President in Egypt’s history has moved on to tackle the big guns. On Sunday, Morsy fired Field Marshal Mohamed Hussein Tantawi, the country’s Defense Minister and powerful chief of Egypt’s military council, with whom the President has been locked in a power struggle since he took office at the end of June. Perhaps no more.

Along with Tantawi, who in the 18 months since the ousting of President Hosni Mubarak has reigned as the most powerful man in Egypt, Morsy sacked his chief of staff, Sami Anan. He fired the head of every service of the armed forces and nullified the June constitutional decree that Tantawi and Anan’s Supreme Council of the Armed Forces (SCAF) had released to seize more power for itself. Morsy also appointed a much anticipated Vice President: Mahmoud Mekki, a prominent reformist judge.

If all that comes as a shock to many Egyptians — the Ramadan-subdued streets of Cairo flickering to life with murmurs of excitement shortly after the announcement — it wasn’t a shock to everyone. That includes the military council. General Mohamed al-Assar, a ranking member of SCAF, told al-Jazeera that Tantawi and Anan’s dismissal came through consultation with Morsy. Analysts say that’s because there was a deal involved. “I think the deal is [Tantawi and Anan] get a safe exit, and they hand the country to the Muslim Brotherhood,” says Mamdouh Hamza, a prominent businessman and pro-democracy advocate. “Because quite honestly, if we apply the same law [to the generals] that we applied to Mubarak’s family, Tantawi would be behind bars.”

The notion that immunity may have been exchanged for power troubled some of the country’s liberal youth as well, even as many other Egyptians flocked to Cairo’s Tahrir Square to celebrate what appeared to be the end of an era. “Morsy clearly won’t prosecute any murderers or torturers,” quipped Gigi Ibrahim, a young activist, on Twitter, following the announcement.

But the bigger picture is this, Hamza says: the reshuffle plays into the broader strategy of Morsy’s powerful Islamist alma mater, the Muslim Brotherhood, which most analysts agree is still calling the shots in the presidential kitchen. “They are the only ones in the kitchen, 100%,” says Hamza. “In fact, Morsy might only be the coffee boy in the kitchen.”

Long the only significant challenge to Mubarak’s 30-year rule, the Muslim Brotherhood emerged from last year’s uprising primed to become the largest political force. Its representatives won the lion’s share of parliament; and ultimately, it took the presidency too.

Sunday’s shift marks Morsy’s boldest move yet to reclaim power from the country’s powerful military council. But it follows a similar reshuffle last week in Egypt’s security sector, which included the ousting of an old regime ally, Mourad Mwafi, from the head of the country’s General Intelligence Service. The replacements in the security sector, and indeed in the military, all serve a purpose in the broader scheme of things, analysts say. “The Muslim Brotherhood doesn’t do anything off the cuff. Everything is according to plan and may be known for a few months before,” Hamza says.

Tantawi’s replacement, Abdel Fatah el-Sissi, is rumored to be a deeply religious man — perhaps the closest thing on the council to a Brotherhood ally. The new Vice President, Mekki, a top judge, was an early — but secret — Brotherhood pick for the presidency, according to Mohamed Soudan, a high-ranking Brotherhood official in Alexandria.

Along with Morsy’s newly appointed Justice Minister, Mekki will be a valuable asset as the country moves forward in drafting a new constitution. And according to Robert Springborg, an expert on the Egyptian military and a professor at the Naval Postgraduate School in California: for every new hire — perhaps regardless of origin — Morsy and the Brotherhood gain an ally. “It’s Morsy and the Muslim Brotherhood who appointed them,” he says. “So their political careers are dependent on Morsy.”

Indeed, that may also be true for the new editors in chief of the country’s state newspapers — appointed last week by the Brotherhood-dominated upper house of parliament, the Shura Council.

The Brotherhood, analysts say, is slowly and deliberately arranging Egypt’s political chessboard. “They had to make sure that the media is in their hands and that the army is under their control before they go and make major changes in the Ministry of Justice and in the justice system,” says Hamza. “The next step will be the new constitution.”

The bold moves, particularly Morsy’s annulment of the military council’s June addendum to Egypt’s constitution — which had granted the military full legislative and certain executive powers — raises some questions of legality, experts say.

“It’s extralegal,” says one foreign NGO worker in Cairo, who has charted similar declarations by the military over the past 18 months. Morsy didn’t nullify all of SCAF’s decrees — only the aspects that hindered presidential power. Whereas the military had, in June, claimed full legislative authority following the Supreme Court’s dissolution of the parliament, Morsy now claims legislative control for himself. He also seized the right — from the generals — to dissolve and replace the committee tasked with drafting Egypt’s new constitution, if the committee is somehow “prevented from doing its duties,” the state-backed Ahram Online news website reported.

Egypt’s powerful generals have largely ignored Egyptian law ever since they issued their first constitutional decree in February 2011, two days after Mubarak stepped down, the NGO official points out: “So why can’t Morsy do it too?” Last February, SCAF suspended Egypt’s 1971 constitution. “They did this to legitimize their own power,” the official adds, because the constitution had stipulated that in the absence of a President, power be handed to the head of parliament or the head of the Supreme Court. Tantawi and his generals had ensured that wouldn’t happen.

But now Morsy may be following in their footsteps. The Islamist President appears — “on paper” at least — to have suddenly amassed “dictatorial powers,” writes Issandr El Amrani, a regional analyst, on his popular blog, the Arabist. For a country still struggling to shrug off the entrenched influence of its military after more than half a century of military rule, that might not be such a terrible thing, El Amrani and other analysts note. Hamza says it’s an important first step in dismantling a junta; if Morsy can remove the military from business and the public sector too, Egypt will be on its way to success, he says. But there’s no telling just how the President and the Brotherhood will move next. As for the paradigm shift and the new powers it seems to entail, says El Amrani: “It will largely come down to how he uses them.”